Transfer files from the PCIMA card to the Dropbox folder on the computer and run the RScript to quality check THE SAME DAY you take measurements. You may think you have perfect memory now, but you will forget! Record electronically which file numbers belong to which plots, reference, or dark scans in the File Key and delete any unnecessary files.

EXPORT THE DATA

Transfer the data from the memoroy card in the unispec device to the LTER RA computer/onedrive.


  1. Remove PCIMA card from Unispec DC

    • Eject the card by pressing the small black button next to the memory card on the back of the device.

    • The memory card is contained within an adapter, carefully pull the card out of the adapter

  2. Insert card into reader with USB connection to computer

    • Be careful to align the PCIMA card properly to avoid bending any of the metal prongs on the connector!!
    • If this occurs, you can straighten with pliers & reinsert card to realign. 

  3. Transfer data folders to computer. Move folders named with (YYYY-MM-DD) containing SITE_XXXXX.spu files to appropriate location in OneDrive/Dropbox.

  4. Fill out Unispec Key, add notes & file numbers to [YEAR_unispec_key.csv] excel sheet.

QUALITY CHECK

Use the RShiny app created by Jim Laundre to check the quality of the data.

  1. Open the Unispec Shiny App

  2. Click “Browse” under “Upload .spu files” and select all the .spu files within today’s date folder

  3. CLick “Browse” under “Upload Field Key Excel files” and select the field key you created for today


TIPS/Troubleshooting:

  1. Missing/mislabeled files. Human error is real. You hopefully kept track of file number / plot correspondence in the field; however, if you get back to lab and something doesn’t line up, there are several tricks you can use.

    1. Look at measurement times. Using the “unispec_quality_check.R” file, look at the times you took each measurement. One line of code will give you a dataframe with the difference in time between each measurement. Usually, you can tell which 5 measurement you took at a single plot (small difference in times) and when you moved between plots (longer times) or blocks (even longer) depending on how far you have to walk.  
    2. Check spectra. You may have simply be off by one due to mislabeled reference or dark scans. Check the spectra of any subset of file numbers to make sure

APPENDIX A. Unispec Location Anomalies

List of irregular unispec locations:

  1. WSG-outlet locations are along the entire side of the plot not confined to 5m, to avoid water.
  2. COMPILE DESCRIPTIVE LIST HERE. BE SPECIFIC.

OLD PROTOCOL:

  1. Open [“process_unispec_files.Rmd”] R Markdown notebook in RStudio. Work through the document to:

    1. Quality Check data by:

      1. Choose white references and update unispec Key [YEAR_unispec_key.csv] (File Numbers for rows where Treatment = REF) 
      2. Exclude bad data with maxed out spectra or other issues.

    2. Calculate vegetation indices [“process_unispec_files.Rmd”] markdown notebook.

  2. Save data to [CONSULT JIM/LAURA ON FILEFORMAT / LOCATION]

  3. Add data to Shiny App to compare with other years by moving updated dataframe into [“shiny_unispec”] directory housing web application. Publish application to the web using RStudio, access at: [https://rubytessa.shinyapps.io/shiny_unispec/]